The permeation of ions through channel proteins is influenced by many structural parameters. Among them are the composition of the bathing electrolytes, the structure of the water–membrane interface, the packing of the phospholipid, the folding of the channel protein, and the structure of the pore–water interface. There is uncertainty regarding both the structural and force field parameters needed to describe ionic interaction with channel-forming proteins. No single model calculation has included enough features of the real physical situation, even for a pore former as simple as gramicidin, to provide a definitive theoretical picture of selectivity. However, by comparing the results of calculations based on different reasonable models of the ion–water–gramicidin system, significant interpretive insights can be gained. As more structural proposals for describing the selectivity regions of physiologically important channel-forming proteins become available, ab initio methods can be used to construct permeation-free energy profiles and test various models. © 1988 Academic Press, Inc.
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